I found the same thing yesterday. I've had my Neo 2.5 years and yesterday saw one of the bolts on the floor as well. I took photos of the bolt and holes on the Neo and sent them to tacx asking them if anything is likely to fall into the drive, how I can remove the part bolt to get it fixed and if it is safe to still ride. Not yet had a reply will post when I do.

we are sorry to hear that. This will not cause any problems on the unit. Keep the part inside
If you want, but we would not advise to do that now, we can exchange and repair it in the future but we suggest to do this in may or so, due to the busy season (could take a while before you have your trainer back)